Sendu Bala
and 1 contributors

NAME

Bio::DB::EUtilities::efetch - retrieval of records from a list of IDs or the user's environment.

SYNOPSIS

  my $efetch = Bio::DB::EUtilities->new(
                                       -verbose => 1,
                                       -cookie   => $esearch->next_cookie,
                                       -retmax   => $retmax,
                                       -rettype  => 'fasta'
                                        );

  print $efetch->get_response->content;

DESCRIPTION

EFetch retrieves data records from a list of ID's. This can be accomplished directly (using id) or indirectly (by using a Cookie.

NCBI Efetch Parameters

The following are a general list of parameters that can be used to take advantage of Efetch. Up-to-date help for Efetch is available at this URL (the information below is a summary of the options found there):

  http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
db

One or more database available through EUtilities. EFetch currently only supports database retrieval from the following databases:

pubmed, pmc (PubMed Central), journals, omim, nucleotide, protein, genome, gene, snp (dbSBP), popset, and taxonomy.

Also supported are sequences (nucleotide, protein, popset and genome), and the three subsets of nucleotide: nuccore, nucest, nucgss

id

a list of primary ID's

Below are a list of IDs which can be used with EFetch:

For sequence databases:

NCBI sequence number (GI), accession, accession.version, fasta, GeneID, genome ID, seqid

All other databases:

PMID (pubmed), MIM number (omim), GI number (nucleotide, protein), Genome ID (genome), Popset ID (popset), SNP cluster ID (snp), UniSTS ID (unists), UniGene cluster ID (unigene), MMDB-ID (structure), PSSM-ID (cdd), 3D SDI (domains), TAXID (taxonomy), GEO ID (geo)

mindate, maxdate

limits results by dates (yyyy/mm/dd format, or by year)

rettype

Output type based on the database. Not all return types are compatible with all return modes (-retmode). For more information, see the specific literature or sequence database links at URL above.

Literature databases have the below return types:

uilist (all databases), abstract, citation, medline (not omim), full (journals and omim)

Literature databases have the below return types:

native (full record, all databases), fasta, seqid, acc (nucleotide or protein), gb, gbc, gbwithparts (nucleotide only), est (dbEST only), gss (dbGSS only), gp, gpc (protein only), chr, flt, rsr, brief, docset (dbSNP only)

retmode

EFetch is set, by default, to return a specific format for each Entrez database; this is set in the %DATABASE hash in Bio::DB::EUtilities. To override this format, you can set -retmode. The normal return modes are text, HTML, XML, and ASN1. Error checking for the set return mode is currently not implemented.

report

Used for the output format for Taxonomy; set to uilist, brief, docsum, xml

strand - sequence only

The strand of DNA to show: 1=plus, 2=minus

seq_start, seq_stop - sequence only

the start and end coordinates of the sequence to display

complexity - sequence only

The GI is often part of a biological blob containing other GIs

    * 0 - get the whole blob
    * 1 - get the bioseq for gi of interest (default in Entrez)
    * 2 - get the minimal bioseq-set containing the gi of interest
    * 3 - get the minimal nuc-prot containing the gi of interest
    * 4 - get the minimal pub-set containing the gi of interest

Additional (Bioperl-related) Parameters

These are Bioperl-related settings and are not used as CGI parameters when

eutil

The relevant EUtility to be used (efetch).

Uses a Cookie-based search (see below)

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@lists.open-bio.org               - General discussion
  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web.

  http://bugzilla.open-bio.org/

AUTHOR

Email cjfields at uiuc dot edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

parse_response

 Title   : parse_response
 Usage   : $db->_parse_response($content)
 Function: parse out response for cookie
 Returns : empty
 Args    : none
 Throws  : 'unparseable output exception'